Lichens are symbiotic organisms comprised of a fungus, mycobiont, and a photosynthetic partner, photobiont. In some cases, cultures of lichen mycobionts have an ability under osmotically stressed conditions to produce new substances. It was pointed out that cultures of lichen mycobionts could be new sources of bioactive compounds. In the course of our studies on cultured lichen mycobionts, we cultivated mycobionts of the lichens collected in Japan and investigated their metabolites. From the cultures of Graphis proserpens, three new isocoumarins and three novel compounds derived from naphthopyrones through an oxidative ring cleavage were isolated along with six known compounds. From the cultured mycobionts of Graphis connectans, three new compounds were obtained and their structures were also elucidated.The diverse metabolites of the cultured mycobionts have never been found in the lichenized state. The finding suggested that the secondary metabolism of mycobionts could be influenced by the algal partner in symbiosis. We investigated the conditions which trigger re-synthesis of the isolated mycobiont and photobiont. In the mixture of both symbionts cultured together on agar medium, mycobiont colonies were in contact with the surface of the algal layer, but neither mycobiont species penetrated the algal cells. On the other hand, the attachment between the mycobiont and algae in the liquid medium was observed and in the center of the mixture, branched mycobiont hyphae often penetrated algal cells. The combination between algae and mycobionts in some experiments was different from the natural lichens and this mismatch may explain the occurrence of parasitism instead of symbiosis. Further studies to elucidate the factors which induce the re-synthesis of the two components could give important information about the symbiosis of lichens and good tools for the production of useful secondary products.